Chlamydiae are a diverse group of obligate intracellular prokaryotic pathogens that infect a wide spectrum of mammalian hosts. Paradoxically, this broad spectrum of infection and disease diversity occurs despite considerable conservation in chlamydial genome organization and structure. To better understand the genetic basis of chlamydial host tropism we have undertaken a comparative in vivo and in vitro functional genomic study of chlamydial host cell interactions. We find that chlamydiae have co-evolved specific virulence genes that function in a species-specific manner to evade IFN-gamma mediated host defense mechanisms. These findings have important implications for the design of humanized mice for the study of C. trachomatis pathogenesis, immunity, and vaccine development.[unreadable] [unreadable] We have shown that chlamydial virulence genes localize to the replication termination region of the genome. This region exhibits extensive genetic polymorphisms among strains and as such has been termed the plasticity zone (PZ). We have mapped and characterized genes within the PZ that confer host specific infection tropism and have identified the host genes targeted by these virulence factors. Specifically we have shown that human strains have maintained a functional tryptophan synthase (TS) operon that circumvents the effect of IFN-gamma mediated indoleamine 2,3-dixoygenase tryptophan deprivation in human cervical epithelial cells. The TS gene is unique to human strains and the IFN-gamma inducible IDO defense system unique to human epithelial cells; demonstrating an unambiguous biological connection supporting the coevolution of pathogen and host. Similarly, we have discovered that the genetically syntenous murine strains have evolved a completely different pathogen strategy for evading IFN-gamma mediated host specific defense in murine epithelial cells. This involves the secretion of a large cytotoxin located in the PZ, unique to murine strains, that targets and inactivates members of the murine specific IFN-gamma inducible small p47 GTPases; specifically the p47 GPTase Iigp1, a G protein that functions in the intracellular trafficking of lipids to the trans-Golgi. To our knowledge this is an unprecedented finding in the field of bacterial pathogenesis because it demonstrates that a restricted complement of pathogen specific genes have evolved specifically to target host-specific IFN-gamma inducible host defense mechanisms; a pathogenetic strategy that defines host infection tropism. Thus, chlamydial PZ virulence genes represent novel targets for the development of new chlamydial anti-infectives and vaccines.